Collaborative analysis of multi-gigapixel imaging data using Cytomine

This is the "advance access" version of an article accepted for publication in Bioinformatics Journal following peer review. The version of record doi: 10.1093/bioinformatics/btw013 will be available online at: http://http://bioinformatics.oxfordjournals.org/

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Abstract :

[en] Motivation: Collaborative analysis of massive imaging datasets is essential to enable scientific discoveries. Results: We developed Cytomine to foster active and distributed collaboration of multidisciplinary teams for large-scale image-based studies. It uses web development methodologies and machine learning in order to readily organize, explore, share, and analyze (semantically and quantitatively) multi-gigapixel imaging data over the internet. We illustrate how it has been used in several biomedical applications. Availability: Cytomine (http://www.cytomine.be/) is freely available under an open-source license from http://github.com/cytomine/. A documentation wiki (http://doc.cytomine.be) and a demo server (http://demo.cytomine.be) are also available.

Research center :

Systems and Modeling

Disciplines :

Computer science

Author, co-author :

Marée, Raphaël ; Université de Liège > Electrical Engineering and Computer Science > GIGA-Research

Rollus, Loïc; Université de Liège - ULiège > Electrical Engineering and Computer Science > GIGA-Research

Stévens, Benjamin; Université de Liège - ULiège > Electrical Engineering and Computer Science > GIGA-Research

Hoyoux, Renaud ; Université de Liège > GIGA-Research

Louppe, Gilles ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Big Data

Vandaele, Rémy ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique

Begon, Jean-Michel ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique

Kainz, Philipp; Medical University of Graz > Institute of Biophysics

Geurts, Pierre ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Algorith. des syst. en interaction avec le monde physique

Wehenkel, Louis ; Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Systèmes et modélisation

Language :

English

Title :

Collaborative analysis of multi-gigapixel imaging data using Cytomine

Publication date :

10 January 2016

Journal title :

Bioinformatics

ISSN :

1367-4803

eISSN :

1367-4811

Publisher :

Oxford University Press - Journals Department, Oxford, United Kingdom

Pages :

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

http://www.cytomine.be

Name of the research project :

CYTOMINE

Funders :

DGTRE - Région wallonne. Direction générale des Technologies, de la Recherche et de l'Énergie [BE]

Available on ORBi :

since 14 January 2016

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